Man pages for erflynn/exprsex
Rank-Based Sex Labeling of Microarray Expression Data

dot-check_entrez_overlapCount the length of overlap with entrez ids for a sequence of...
dot-checkExprMatFormatChecks that an input expression matrix has the correct format
dot-checkFitFormatChecks that a fit object has the correct structure
dot-checkGeneFormatChecks that the expression matrix rownames contain the genes...
dot-checkMatchingChecks that sex labels and expression matrix match
dot-checkProbeMappingChecks that a probe mapping has the correct format.
dot-checkSexLabFormatChecks that input sex labels have the correct format
dot-checkTrainInputFormatChecks that expression matrix and sex labels have the correct...
dot-clean_mappingClean up the mapping output
dot-convertGenesConvert the expression matrix to genes. This takes the...
dot-detect_ensembl_colsIdentify the ensembl columns and return the one with the max...
dot-detect_entrez_ids_nameLooks for entrez ids by trying to find a column name named...
dot-detect_genbank_colsIdentify the genbank columns and return the first (Note -...
dot-detect_genbank_cols_nameLooks for genbank cols by trying to find a column name named...
dot-detect_hgnc_colsIdentify the HGNC columns and return the first (Note - this...
dot-detect_int_colsIdentify integer only only columns, hopefully these are...
dot-detect_refseq_colsIdentify the refseq columns and return the one with the most...
dot-detect_unigene_colsIdentify the unigene columns and return the one with the most...
dot-expDataToRanksConvert an expression dataset to ranks.
dot-extract_biomart_refExtract a gene mapping table from biomaRt, this contains...
dot-extract_entrezGets a list of all entrez ids for an organism. This pulls the...
dot-filterGenesByVarHelper function to filter genes based on their standard...
dot-find_col_locHeper function to find the location within a column of an ID....
dot-find_entrez_w_in_blockIdentify columns that might have entrez in them. This would...
dot-geomMeanAcrossGenesHelper function to calculate geometric mean of a set of genes...
dot-geomMeanScoreCalculate the score geometric mean of male genes - female...
dot-get_genbankGets a mapping of genbank to entrez. Note - these tables are...
dot-get_ref_dataGenerate the desired mapping data for that organism
dot-get_unigeneGets a mapping of unigene ids to entrez ids. This pulls the...
dot-get_xy_genesGets a table of all the X,Y genes for that organism with the...
dot-load_refLoad the desired reference data mapping table. The reference...
dot-map_from_ensemblHelper function to extract and map ensembl to entrez
dot-map_from_genbankHelper function to extract and map genbank to entrez
dot-map_from_hgncHelper function to extract and map HGNC to entrez Note - this...
dot-map_from_refseqHelper function to extract and map refseq to entrez
dot-map_from_unigeneHelper function to extract and map unigene to entrez
dot-my_assertCustom assertion function, prints formatted error messages...
dot-parse_multi_colHelper function to parse a pattern out of a multi-column....
dot-reform_entrez_dfHelper function to reformat entrez gene/probe data frame....
dot-reorderGeneMatReorder the expression matrix so it contains the...
exprsexexprsex: A package for sex labeling microarray expression...
generate_all_refCode to generate all reference tables for rat, mouse, and...
getConsensusGenesCreate a consensus gene list from a set of expression...
getPrepGSEGet and prepare a gse file for sex labeling by converting it...
map_mult_gplWrapper to parse and map data from multiple gpls.
parse_entrez_from_gplParse and map entrez data from a GPL annotation.
predSexLabUse a particular sex labeling fit to label an input dataset
prepFromExprPrepare data from an existing expression matrix
reorderRankReorder and rank a gene expression matrix. We then use this...
runSexLabRun sex labeling using default settings.
sex_lab_genesDefault genes used for sex labeling.
trainSexLabTrain a sex labeling classifier using input training data.
erflynn/exprsex documentation built on Jan. 26, 2020, 10:07 a.m.